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comparison MzMLSplitter.xml @ 6:b14efb4cf1ea draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
author galaxyp
date Tue, 20 Mar 2018 15:23:48 -0400
parents 6caab3e848d2
children ab079a6757c1
comparison
equal deleted inserted replaced
5:6caab3e848d2 6:b14efb4cf1ea
5 <description>Splits an mzML file into multiple parts</description> 5 <description>Splits an mzML file into multiple parts</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">MzMLSplitter</token> 7 <token name="@EXECUTABLE@">MzMLSplitter</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
10 <expand macro="references"/> 10 <expand macro="requirements"/>
11 <expand macro="stdio"/> 11 <expand macro="stdio"/>
12 <expand macro="requirements"/> 12 <command><![CDATA[
13 <command>MzMLSplitter 13 mkdir parts/ &&
14
15 MzMLSplitter
14 16
15 #if $param_in: 17 #if $param_in:
16 -in $param_in 18 -in $param_in
17 #end if 19 #end if
18 #if $param_out: 20 #if $param_out:
19 -out "$param_out" 21 -out "parts/$param_out"
22 #else
23 -out "parts/MzML"
20 #end if 24 #end if
21 #if $param_parts: 25 #if $param_parts:
22 -parts $param_parts 26 -parts $param_parts
23 #end if 27 #end if
24 #if $param_size: 28 #if $param_size:
41 #if $adv_opts.adv_opts_selector=='advanced': 45 #if $adv_opts.adv_opts_selector=='advanced':
42 #if $adv_opts.param_force: 46 #if $adv_opts.param_force:
43 -force 47 -force
44 #end if 48 #end if
45 #end if 49 #end if
46 &gt; $param_stdout 50 -threads "\${GALAXY_SLOTS:-1}"
47 </command> 51 ]]></command>
48 <inputs> 52 <inputs>
49 <param name="param_in" type="data" format="mzml" optional="False" label="Input file" help="(-in) "/> 53 <param name="param_in" type="data" format="mzml" optional="False" label="Input file" help="(-in) "/>
50 <param name="param_out" type="text" size="30" label="Prefix for output files ('_part1of2.mzML' etc" help="(-out) will be appended; default: same as 'in' without the file extension)"> 54 <param name="param_out" type="text" size="30" label="Prefix for output files ('_part1of2.mzML' etc" help="(-out) will be appended; default: same as 'in' without the file extension)">
51 <sanitizer> 55 <sanitizer>
52 <valid initial="string.printable"> 56 <valid initial="string.printable">
67 <expand macro="advanced_options"> 71 <expand macro="advanced_options">
68 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 72 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
69 </expand> 73 </expand>
70 </inputs> 74 </inputs>
71 <outputs> 75 <outputs>
72 <data name="param_stdout" format="txt" label="Output from stdout"/> 76 <collection name="parts" type="list">
77 <discover_datasets pattern="__name_and_ext__" format="mzml" directory="parts" />
78 </collection>
73 </outputs> 79 </outputs>
80 <tests>
81 <test>
82 <param name="param_in" value="FileFilter_1_input.mzML"/>
83 <param name="param_parts" value="2" />
84 <output_collection name="parts" type="list">
85 <element name="MzML_part1of2" file="MzMLSplitter_output_part1.mzML" ftype="mzml" />
86 <element name="MzML_part2of2" file="MzMLSplitter_output_part2.mzML" ftype="mzml" />
87 </output_collection>
88 </test>
89 </tests>
74 <help>Splits an mzML file into multiple parts 90 <help>Splits an mzML file into multiple parts
75 91
76 92
77 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MzMLSplitter.html</help> 93 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MzMLSplitter.html</help>
94 <expand macro="references"/>
78 </tool> 95 </tool>